Normally, fit, rms, and rms_cur require that all atom identifiers match.  However, we're trying to increase flexibility by supporting alternate pairwise "matchmakers"...assuming (A) that you're running 1.2 beta 3 and (B) that the atom names match:
rms_cur m1, m2, matchmaker=4
may work.  To visualize the mapping (for verification):
rms_cur m1, m2, matchmaker=4, object=alignment

From: Evan Kantrowitz [mailto:evan.kantrowitz@bc.edu]
Sent: Tuesday, March 10, 2009 7:59 AM
To: PyMOL-users@lists.sourceforge.net
Subject: [PyMOL] Trying to get rms and rms_cur to run

Hi Folks,

    I have two positions of one small molecule.  I am trying to determine the RMSD between them without doing an align

I read the molecules into pymol as m1 and m2.  As seen below each has 23 atoms.  When I do an rms it gives the error: No atoms selected, but if I do an align it it fine.  Can anyone help with why the rms does not work?

PyMOL>sele a, m1
 Selector: selection "a" defined with 23 atoms.

PyMOL>sele b, m2
 Selector: selection "b" defined with 23 atoms.

PyMOL>rms m2, m1
ExecutiveRMS-Error: No atoms selected.

PyMOL>align m2, m1
 Match-Warning: unknown residue type 'AMP' (using X).
 Match-Warning: unknown residue type 'AMP' (using X).
 Match: read scoring matrix.
 Match: assigning 1 x 1 pairwise scores.
 MatchAlign: aligning residues (1 vs 1)...
 ExecutiveAlign: 23 atoms aligned.
 ExecutiveRMS: 1 atoms rejected during cycle 1 (RMS=0.37).
 Executive: RMS =    0.333 (22 to 22 atoms)

PyMOL>rms m2, m1
ExecutiveRMS-Error: No atoms selected.

Evan R. Kantrowitz, Ph.D                                                                  evan.kantrowitz@bc.edu
Boston College                                                                                   Tel. 617-552-4558
Department of Chemistry                                                                  FAX 617-552-2705                                      
Merkert Chemistry Center, Rm 239                                                  www2.bc.edu/~kantrow
Chestnut Hill, MA 02467